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As voltage sensitive organic dyes enter the inside of neurons and quantum dots are seeking to replace these due to their higher quantum yield, I was wondering what the seize limit is, as quantum dot are typically dozen of nanometers across in every direction.

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I've used latex microspheres in the past. These not only enter cells but also move retrograde (backward) through axons, and are sized up 0.02 to 0.2 microns; it seems like the smaller beads in the range of 0.05 microns are taken up better (or at least transported better) than the larger ones. You can see the individual spheres clearly on a microscope in labeled cells.

I think it's wrong to think about just size. Not everything will get through membranes. Small hydrophobic materials can just slip through the membrane, but larger ones rely on endocytosis. I don't know if further work has been done on the mechanisms of these tracers, but early papers suggested that they are taken up by endocytosis particularly at presynaptic terminals and then transported as vesicles along microtubules.

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